Hi, we've run into an issue running FS 4.01 on an Altix cluster (SuSE
Itanium distribution -
freesurfer-ia64-unknown-linux-gnu-stable4-20070918). On some subjects
mri_cc falls over with a segmentation fault error (output pasted below).
Running mri_cc -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz
That should be fine (-ccseg -cortribbon -cortparc -aparc2aseg -wmparc).
Allison
On Wed, 23 Jan 2008 [EMAIL PROTECTED] wrote:
Thanks, I'll try that. Will I then need to redo all steps fromm -ccseg
onwards if I want a correct wmparc at the end, or can I safely skip some?
For instance, I could do
Hi Doug,
No, I haven't tried it for this, but I have read the help before. It says this:
"If nnf is chosen, then the value at the target vertex is set to that of the
closest source vertex."
If you wanted to go from a sparsely valued single subject surface (i.e.
decimated dipoles) to ico4, it s
Yes, that's it exactly. It contains a start time in ms for the data, a
timepoint length in ms, the IDs for the vertices and the vert x
timepoint data matrix. It's read in by the mne_analyze tool from the MGH
MEG/minimum-norm toolkit. The matlab toolkit included with the MGH MEG
distribution inc
I'm not even sure what stc is. Is that the multi-frame .w file?
Pádraig Kitterick wrote:
Dear Don and Doug,
Thank you for the suggestions. I have devised a workflow by using .w
files for each timepoint/subject, and then using
mri_surf2surf/mri_concat to average across participants. Ideally,
Thomas,
Have a look at:
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
for info on thickness differences. Be sure to use freesurfer v4.0.2, as
that contains support for .mgh file io for the binaries mentioned on
that page.
Nick
On Wed, 2008-01-23 at 15:36 -0300, Thomas Doeri
Hi,
i am wondering how i can do a comparison of just two subjects (twins),
calculating differences between them in cortical thickness, gm-volume .etc...
I tried to find some paper with a processing pipline for this but without
success...
Perhaps somebody has a hint for me?
Thanks,
Thomas
Hi Mike,
no, this is not the intended behavior, and I think Nick has a fix for it
in the most recent recon-all.
Bruce
On Tue, 22 Jan 2008, Michael Harms wrote:
Hello,
Kristine's earlier post got me wondering why she was "losing" any
previous aseg edits if her data were re-processed under FS
Chris,
The ?.volume files are somewhat misleading in name in that they are not
MRI volumes in the traditional sense. Rather, it is the cortical volume
at a surface vertex, as calculated by multiplying area by thickness.
Doing so requires a new utility called mris_calc, which will be in the
next r
Freesurfers,
The wiki mentions one of the "known issues" with the current release is
that recon-all does not create ?h.volume files. I have been using the
following command to create what appear to be volume files for cortical and
wm parcellations. Is the problem just that these files are not
Dear Don and Doug,
Thank you for the suggestions. I have devised a workflow by using .w
files for each timepoint/subject, and then using
mri_surf2surf/mri_concat to average across participants. Ideally, I
would like to use a study-specific average, so this approach will permit
that.
I do fi
Thanks, I'll try that. Will I then need to redo all steps fromm -ccseg
onwards if I want a correct wmparc at the end, or can I safely skip some?
For instance, I could do -ccseg -cortribbon -cortparc -aparc2aseg -wmparc?
Best,
Kristine
> Kristine,
> You should be able to use -ccseg which occurs a
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